I thought (hoped) they might not charge for the second pump & labour as I would have thought it should be routine (for a plumber) to check the oil feed if a tank has run dry and existing boiler pump gets knackered trying to resume delivery after this? Or am I wrong to think this would have been sensible / routine?
Possibly, but it's also routine to check your oil level and not run out. In any case I'd expect clearing and disposing of 60 litres of oil a far bigger job than supplying & fitting another pump.
In short they should've cleared the oil sediment. After doing so billed you accordingly for the extra work involved.